I'd think that, assuming Japanese victories at the start, that Germany might intervene on Spain's side if it can. Germany has already intervened via the Triple Alliance in 1895, I wouldn't put it past Wilhelm to try and have a go at a second intervention with the aim of siphoning off Taiwan from Japan or something. Exactly how the other great powers might react to this I don't know, too many variables over who might want what and how each reacts to any actions the others take.1898?
Navally it's going to go down to how the Spanish cruisers perform vis a vis the Japanese ones, but the Japanese are coming off the Sino Japanese War with both reinforcements and salvage
The Germans might be more inclined to push their luck if it is Japan rather than the USA
Or you might see Japan act decisively so that the Germans don't even get into the play at Manila
Will the Spanish send the Pelayo?
I think Spain would send the Pelayo in this instance, Japan wouldn't/doesn't have the power projection to launch a fleet to Spain's atlantic coast in Spain's eyes, so they'd be more confident about forming a taskforce with which to reverse any losses/shore up their position in the pacific.